Sunday, July 31, 2011

Entering burning forests and buildings is a dangerous job. Being able to track each firefighter’s position and vital signs would make that job a little less dangerous. Unfortunately, radio and GPS signals are often lost deep inside structures or forests. Researchers from the University of Virginia and from Oceanit Laboratories of Honolulu are now testing a new communication system that will allow commanders to monitor their firefighters in real time.

The system is composed of three distinct parts, nicknamed WISPER, GLANSER and PHASER. First, WISPER. These Wireless Intelligent Sensor Platform for Emergency Responders are tiny routers that are waterproof and heat resistant to 500° F. A firefighter would carry five of the one-inch square nodes in a special canister. Each time the base station loses contact with the firefighter, the canister automatically drops a router.

The firefighters would also carry Geospatial Location Accountability and Navigation System for Emergency Responders (GLANSER), and Physiological Health Assessment System for Emergency Responders (PHASER), devices that display their exact location and their vital signs. Both GLANSER and PHASER would use WISPER routers, dropped at strategic locations, to allow commanders to monitor the position and health of their crews.

The system has been successfully tested in simulations. Now the developers are looking for a large-scale manufacturer.

Top-left: One inch-square WISPER routers.

Center-left: When cued by the base station, a motor-powered dispenser will drop a WISPER node.

Bottom-left: A USB-powered base station plugged into a laptop monitors each node’s strength, reroutes traffic around a weak or dead node, and commands a dispenser to drop a node.

Right: Using the Network Coordinator software, a fellow firefighter can warn a colleague whose dispenser is running out of nodes or battery life. The software also displays and stores each firefighter's location and vital signs beamed over WISPER by GLANSER and PHASER.

Friday, July 29, 2011

Ever since the human genome was sequenced over a decade ago, people have been wondering when this new font of information would be used to treat disease. For the Beery family, that day is today.

At age two, the Beery twins were diagnosed with cerebral palsy. However, as the children grew, it became clear that this diagnosis did not explain their symptoms. At six, they were rediagnosed with a disease called ‘dopa-responsive dystonia’, which is treatable by administering the neurotransmitter dopamine. This worked until the kids were in their teens, when one of them began to have breathing problems.

At this point, the children’s mother brought them to the Baylor Human Genome Sequencing Center for genetic analysis. Both twins, their parents and the twins’ older brother had their genomes sequenced. The geneticists found that the twins had inherited two dysfunctional copies of the gene for sepiapterin reductase (SPR). In other words, each of their parents had one mutated copy of the gene and one normal copy, and the twins were unlucky enough to have inherited both mutated copies. SPR is not only responsible for dopamine production, but also for the production of serotonin and noradrenalin, two other neurotransmitters.

Upon acquiring this new information, the children’s doctor began supplementing the twins with not only dopamine, but also serotonin. Within a month, the twins showed a dramatic improvement. To be clear, this treatment protocol was chosen specifically because of the sequencing data. Without the genome sequences of the family, doctors would never have known to take this course of action.

Interestingly, the two parents had two completely different mutations in their SPR genes. The father’s mutation led to a protein with the wrong amino acid inserted in the middle, whereas the mother’s mutation led to a severely shortened protein. The researchers speculate that the two types of mutation may be responsible for different, though less severe symptoms in the parents.

Echolocating dolphins emit high frequency sounds (ultrasounds) from organs within their foreheads. These sound beams bounce of any objects (sea floor, predator, prey etc.) in their path and the resulting echo is interpreted by the animal’s brain. Although researchers knew that dolphins had two sound producing organs, it was assumed that only one was functional at a time. Either both organs can function simultaneously, or some other process within the dolphins’ heads is dividing up single pulses. In either case, more than one signal is leaving the dolphins’ heads.

Why send out two pulses? As Starkhammer explains:

The beam projections have different frequencies and can be sent in different directions. The advantage is probably that the dolphin can locate the object more precisely.

Wednesday, July 27, 2011

Cleaning valuable works of art is an extremely tricky process. The restorer must remove dirt and salts without damaging the original paint or substrate. Researchers from the Polytechnic University of Valencia, in conjunction with the restorers of the Sistine Chapel, have been using bacteria to help them clean murals.

The technique was first developed by University of Molise microbiologist Giancarlo Ranalli. Briefly, the scientists apply a thin layer of gel containing the bacteria Pseudomonas to the artwork. After about two hours, the gel is removed from the surface and any remaining bacteria are killed by the resulting dry environment. During those few hours, the bacteria eat the white salt crusts that obscure the paintings.

Thus far, the technique has been successfully tested on two of the ceiling vaults in the heavily damaged Church of Santos Juanes (which had sustained both a devastating fire in 1936 and an improper restoration in the 1960’s). The researchers plan to experiment with other strains of bacteria to remove other types of dirt or decomposition products.

Pilar Bosch of the Institute of Heritage Restoration working on the paintings in the Church of Santos Juanes in Valencia.

As planets form around a star, they sweep together all the dust and rocks at their radius from that star. The debris at that distance is gradually incorporated into that planet. Because Mars has a larger orbit than the Earth, it should have had that much more material in its path and consequently, it should have been larger than the Earth. In actuality, Mars is only a little over half as big as the Earth.

According to this new theory, early in the formation of the solar system, currents of gas pulled Jupiter inward from its birth position at 3.5 AU (astronomical units, one of which equals the distance from the Earth to the sun) to about 1.5 AU from the sun, exactly where Mars would eventually sit. As Jupiter rolled through that region, it gathered much of the available debris to itself, depriving the early Mars of planet-building material and stunting its growth. The interesting thing is that Jupiter then made an about face, probably because of Saturn’s pull, and moved back out to its current position at 5.2 AU. This pattern of movement has been dubbed the ‘Grand Tack Scenario’. As Walsh explains:

This change in direction is like the course that a sailboat takes when it tacks around a buoy.

New evidence from exoplanet research shows that gas giants do migrate inward and back out from their stars, so the Grand Tack Scenario is more likely than it sounds at first glance. In fact, it may explain the distribution of asteroids throughout the solar system.

Monday, July 25, 2011

Rods and cones are light sensing cells that allow us to see. Now thanks to innovations led by Alfredo Dubra of the University of Rochester, we can see the rods and cones.

Caption: The image on the left shows the smallest cones at the center of the retina, (the fovea). Whenever we direct our gaze at something, for example to read, the image of what we are looking at is formed over these very important cones. The image on the right shows a more eccentric retinal location, in which the large bright dots with a dark ring around them are cones, and the surrounding (and far more abundant) smaller spots are rods.

Credit: University of Rochester/Biomedical Optics Express

The researchers used ‘adaptive optics’ a tool developed by astronomers to make distortion free images of stars. In astronomy, a bright point, either a nearby star or focused laser, is used as a reference. The adaptive optic system then uses a deformable mirror to compensate for atmospheric distortions, effectively eliminating the twinkling effect of stars. This substantially increases a telescope’s resolution. In the same way, using mirrors to compensate for the distortion created as light passes through the front of the eye increases the resolution of the ophthalmoscope to the point where individual rod cells can be discerned.

Pal and her colleagues used participants who were already enrolled in the Kronos Early Estrogen Prevention Study (KEEPS), an ongoing study on the relationship between menopausal hormone therapy and heart disease. The 114 subjects of Pal’s study had all had their last period within the past three years, and none had used either hormone replacement therapy or cosmetic surgery. Both the depth and number of wrinkles in eleven locations across the face and neck, and the skin rigidity on forehead and cheeks were assessed for all 114 volunteers. In addition, the women were tested for skeletal mass and density. Skin rigidity correlated positively with bone density, but wrinkles did not.

As Pal states:

The worse the wrinkles, the lesser the bone density, and this relationship was independent of age or of factors known to influence bone mass.

Although it’s a bit depressing to think that our wrinkles are indicating aging inside as well as outside, there is a silver (gray?) lining. If these results are confirmed in larger studies, it could give doctors a quick way to assess which women should be monitored more closely for osteoporosis.

Friday, July 22, 2011

The classical cooperation study used in chimpanzees and young children requires two individuals to perform a task. The two animals each must pull on a rope to bring a cart laden with treats within reach. If only one animal pulls, it will simply draw the rope completely out from around the cart.

The elephant study was conducted by Frans de Waal and his colleagues from Emory University and from the Forest Industry Organization in Lampang, Thailand. You can see some experiments below. Elephants were able to understand that that they must wait for a partner before pulling on their own rope.

The parrot study, led by Dalila Bovet of Paris West University Nanterre La Défense, showed similar results. However, African grey parrots were also able to divvy up two different types of tasks in order to get a reward. For example, one parrot might have to release a tray that the second parrot could then pull closer.

Interestingly, the personalities of the parrots seemed to come into play more than those of the elephants. When given a choice between a small reward that could be earned alone and a larger reward that required cooperation to obtain, two parrots (Zoe and Leo) worked well together but a third (Shango) always chose to work alone. Of course, it’s possible that the elephants in the Thailand study were willing to work together in different combinations because they were all part of the same family group. Like them, Zoe and Leo had been reared together, but Shango had been introduced later.

Our corneas and lenses block UV light from entering our retinas. Excessive amounts of UV light absorption by the cornea results in a painful condition known as photokeratitis, or snow blindness. As the name implies, this condition is common in regions with large amounts of snow, which can reflect up to 90% of UV radiation back into the eyes. Coincidentally, these are also regions where reindeer live.

Perhaps uniquely among mammals, reindeer corneas do not block UV. Rather, that UV light is allowed to pass into the reindeer retina where it triggers the photoreceptors. Reindeer can respond to light at wavelengths down to 320 nm.

It has long been assumed that UV rays would permanently damage the mammalian retina, and that the temporary sacrifice of the cornea to snowblindness was a way to prevent that damage. This reindeer data calls that assumption into question. The reindeer don’t experience snowblindness nor does UV light damage their retinas.

Why do reindeer have the ability to see UV light? Here are a few items that absorb UV radiation and thus would stand out blackly on a snowy field—if anyone could see them: urine, fur and lichens. The former two items could indicate predators or rivals, the latter, lunch.

Wednesday, July 20, 2011

Rob Eagle of Caltech and UCLA and his colleagues from those schools, Universität Bonn, Colorado College, Casper College and the University of Oklahoma have developed a way to take a dinosaur’s temperature by examining its teeth. They found that sauropods had an internal temperature of 36 to 38°C. In comparison, humans have an average body temperature of 37°C.

A year ago, I wrote a post about how researchers had used carbon and oxygen isotopes found in the teeth of modern animals to determine their internal body temperature. Here’s a recap of that explanation:

As new bone is created in living vertebrates, carbon and oxygen (among other elements) precipitate out of the bloodstream and harden into bioapatite, or mineralized bone. A fraction of that carbon and oxygen will be the isotopes 13C and 18O. Those two isotopes will be clumped together if they were deposited at lower temperatures, but spread more randomly through the bioapatite if they were deposited at higher temperatures.

A year ago, the researchers successfully used isotope clumping (or the lack thereof) to determine the body temperature of mammals and reptiles. At that time, they were eager to try their method on fossilized dinosaur teeth. Now they have. Surprisingly, giant sauropads like Brachiosaurs were as warm-blooded as mammals. Next, the scientists plan to see if smaller dinosaurs were equally homeothermic.

Tuesday, July 19, 2011

In many species, either females or males tend to live their whole lives in one area while the other sex disperses soon after reaching maturity. This ensures that genetic diversity is maintained (though of course, the animals aren’t thinking about that). Research on strontium levels in hominid teeth, led by Sandi Copeland of the University of Colorado-Boulder and the Max Plank Institute, suggests that for early hominids, it was the females who left home.

Specific strontium isotope ratios are associated with different types of soils. Those soil isotopes are absorbed by the local plants, and then by the local animals. While some parts of the body are constantly being recycled, tooth formation ends when the tooth is enclosed by enamel. Thus, the strontium isotopes found in an adult molar indicate where that person spent the first eight or so years of life.

The researchers examined 19 teeth from two million year old Australopithecus africanus and Paranthropus robustus individuals for isotopic strontium ratios. The teeth were found in two cave systems located in a region with a distinct strontium ratio. While the larger teeth (presumably from males) displayed that same local ratio, many of the smaller teeth did not. If the authors are correct in assuming that small adult molars belong to females, this strongly suggests that the females had entered the cave systems after childhood.

Monday, July 18, 2011

Congenital generalized hypertrichosis (CGH) is an extremely rare condition of excessive hair growth. You may know it as the somewhat pejorative ‘werewolf syndrome’. Long thought to be a genetic disorder, it has only recently been traced to an insertion in a specific region of the X chromosome.

A team of researchers from the University of Southern California and from various Chinese institutes was able to compare two families, one Mexican and one Chinese, with histories of CGH. The Chinese family members who suffered from CGH had an insertion of a piece of chromosome 5 into region q27.1 of an X chromosome. That means that at some time in the past, a chunk of chromosome 5 had broken off from its usual position. Rather than being stitched back together in the right place back on chromosome 5, the DNA repair mechanisms had stuck the chunk near the tip of the X chromosome. This event had occurred in a stem cell (egg or sperm) and consequently was passed on to future generations.

At this point, it wasn’t clear whether the problem was in the disruption of region q27.1 of the X chromosome, or something specific about the inserted piece of chromosome 5. Then DNA from the Mexican family was sequenced. The CGH patients in that family had an insertion of chromosome 4 into region q27.1 of the X chromosome. Clearly, the problem wasn’t caused by what was added, but rather by the disruption itself.

Both insertions occurred within a palindromic sequence of DNA. Although the significance of this DNA palindrome is not understood, it definitely ceased to read the same way backwards and forwards after the insertion event. In addition, the insertions were near the SOX3 gene, which is a member of a gene family known to be involved in hair growth.

Taken together, the researchers believe that these rare insertion events disrupted a critical palindromic sequence at the end of the X chromosome, which in turn up-regulated (turned on) the SOX3 gene. If so, finding a way to control SOX3 could lead to a cure of both CGH and baldness.

Bees were trained to associate one odor with a sweet reward and another with the unpleasantly bitter taste of quinine. Frankly, just the fact that bees can be trained at all is interesting in and of itself. In any case, if the bee were interested in what might be advertised by the odor, she would extend her mouthparts and try a sample.

Next, some of the bees were subjected to the violent shaking reminiscent of a large animal attacking the hive. Finally, the bees were presented with new odors that could have been connected to either sweet treat or bitter quinine. The shaken bees were much more reluctant to give the novel odors a try. They also had lower levels of dopamine and serotonin. Again, who knew bees even had dopamine or serotonin?

Clearly, the shaken bees were more cautious than those that had not just come off a bad experience. I’m not sure I would take it to the extreme of the authors, who seem to be suggesting that the bees not only display pessimism and agitation, but that:

In terms of what we are able to measure, a shaken honeybee is no less 'anxious' than a lonely dog or a rat in a barren cage.

Personally, I’m not convinced that greater prudence necessarily equates with anxiety. And even if the two are often connected in vertebrates, that doesn’t mean that bees also have those sensations. Still, it’s apparent that bees are surprisingly intelligent and complex.

Saturday, July 16, 2011

Some animals display the most amazing ability to flock together. When they do so, they aren't following a leader, rather each individual is simply maintaining a set distance from its mates. Youtuber bc234 caught these starlings flocking over the Piazza Cinquecento in Rome.

Friday, July 15, 2011

Genetics is the study of DNA sequences. Until the last decade or so, those sequences were believed to be all important in understanding our biological destiny. Now it turns out that chemical changes to our DNA (most notably adding methyl groups) can have profound effects on our wellbeing without any underlying changes in nucleotide sequence. Those chemical changes make up the 'methylome', part of the burgeoning field of epigenetics.

Just as genomic studies required the data set of a few entire genomes, so too does epigenetics require having an epigenetic data base. An international consortium of researchers has just created a DNA methylation map from 1628 human samples, including 424 normal tissues, 1054 cancerous tissues of varying types, and 150 tissues with non-cancerous disorders. Already, these methylomes are producing significant results. For example, there are distinct differences between cancerous and non-cancerous tissues. Neurological and autoimmune diseases also have their own specific methylation profiles.

Besides adding to our understanding of the human condition, these data could have real medical benefits. Even without being able to ‘fix’ methylation so that tumors reverted to normal tissue profiles, the methylation data could help doctors determine the tissue of origin for metastatic tumors, always a plus when pursuing treatment options.

Thursday, July 14, 2011

Although common in bats and dolphins, echolocation is exceedingly rare in humans. The surprising thing is that it’s not nonexistent. There actually are individuals who have learned to echolocate. Melvyn Goodale and Lore Thaler of the University of Western Ontario and Stephen Arnott of the Rotman Research Institute put a couple of blind echolocators in an fMRI to see how they do it.

Natural echolocators, like the two subjects used in the study, often use palatal clicks to produce their echoes. Because the inside of an fMRI scanner offers little opportunity for navigation, the researchers recorded both those clicks and the resulting echoes as they would sound from within the subjects’ own ears. In this way, they could simulate the effect of being in front of various objects. The volunteers would hear the clicks and the echoes as if they were in an open space, rather than in a claustrophobic tube. Two sighted controls were treated in the same manner.

All the participants had normal hearing. However, unlike the sighted people who only used the auditory parts of their brains to process the signals, the blind participants employed their calcarine cortexes (a part of the brain devoted to vision) to make sense of the clicks. In other words, they were literally creating pictures from sounds. Those pictures included details like size, distance, even texture.

Of the two subjects in the study, one has been blind virtually since birth but the other didn’t lose his eyesight until his teens. The fact that both have been able to learn this technique indicates that it could be within the power of most blind people.

Wednesday, July 13, 2011

The perseverative search error seems to be a function of social interaction and not of cognitive development. Perhaps I should elaborate for those of you unfamiliar with this reasoning error (as I was until quite recently).

The perseverative search error, also known as the A-not-B error, is routinely made by children between 8 and 12 months. It goes like this: If you hide an object in location A a few times, and then hide the object in location B, babies will continue to search for the object at A. This is true even if the child clearly sees that the object was placed at B. You can see an example of this highly replicated finding below.

There have been many explanations for this occurrence, including that very young children are cognitively incapable of switching their focus to another location, and that they are incapable of remembering recent events. However, researchers from the Hungarian Academy of Sciences conducted an experiment that rules out those possibilities. Instead, it seems that perseverative search error is a product of social interactions.

The Hungarian scientists performed the A-not-B test in the usual manner, which involves a lot of talking and eye contact. They also ran the tests in situations where the experimenter did not talk to or make eye contact with the child, and in situations where there was no one present with the child. In the first case, they got the usual result, i.e. the child made the A-not-B error most of the time. However, in the latter two tests, babies were fooled less than half the time. In other words, the perseverative error is not a function of babies’ brain development but rather is induced by social contact.

This finding could have implications for all sorts of cognitive studies done on young children. Researchers will have to be sure they are not testing babies' abilities to interact socially rather than their ability to reason.

The physicists took electrons from ytterbium fluoride molecules and subjected them to a finely tuned laser. The energy from that laser causes the electrons to move in specific ways.A spherical electron will rotate differently than an egg-shaped electron, which will tend to wobble.To the limits of their detection capacities, the researchers found no wobble at all.In fact, the complete lack of wobble translates to a difference of less than 0.000000000000000000000000001 cm from being a perfectly sphere. And it could turn out to be a lot less if we still don't detect any wobble as our measuring skills improve.

This data has repercussions for understanding how the universe came to be constructed the way it is.More specifically, the spherical nature of electrons may play a role in determining what happened to all the anti-matter that was presumably formed along with regular matter during the Big Bang.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.